Skip to main content
SpringerLink
Log in

Using ChromEvol to Determine the Mode of Chromosomal Evolution

  • Protocol
  • First Online:
Plant Cytogenetics and Cytogenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2672))

Abstract

The ChromEvol software was the first to implement a likelihood-based approach, using probabilistic models that depict the pattern of chromosome number change along a specified phylogeny. The initial models have been completed and expanded during the last years. New parameters that model polyploid chromosome evolution have been implemented in ChromEvol v.2. In recent years, new and more complex models have been developed. The BiChrom model is able to implement two distinct chromosome models for the two possible trait states of a binary character of interest. ChromoSSE jointly implements chromosome evolution, speciation, and extinction. In the near future, we will be able to study chromosome evolution with increasingly complex models.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 229.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Coghlan A, Eichler EE, Oliver SG, Paterson AH, Stein L (2005) Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet 21:673–682

    Article  CAS  PubMed  Google Scholar 

  2. Khandelwal S (1990) Chromosome evolution in the genus Ophioglossum L. Bot J Linn Soc 102:205–217

    Article  Google Scholar 

  3. Rice A, Glick L, Abadi S, Einhorn M, Kopelman NM, Salman-Minkov A et al (2015) The Chromosome Counts Database (CCDB)–a community resource of plant chromosome numbers. New Phytol 206:19–26

    Article  PubMed  Google Scholar 

  4. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C et al (2009) Polyploidy and angiosperm diversification. Am J Bot 96:336–348

    Article  PubMed  Google Scholar 

  5. Escudero M, Martín-Bravo S, Mayrose I, Fernández-Mazuecos M, Fiz-Palacios O, Hipp AL et al (2014) Karyotypic changes through dysploidy persist longer over evolutionary time than polyploid changes. PLoS One 9:e85266

    Article  PubMed  PubMed Central  Google Scholar 

  6. Raven PH, Kyhos DW (1965) New evidence concerning the original basic chromosome number of angiosperms. Evolution 19:244–248

    Article  Google Scholar 

  7. Stebbins GL (1971) Chromosomal evolution in higher plants. Chromosomal evolution in higher plants. Edward Arnold, London, UK

    Google Scholar 

  8. Grant V (1981) Plant speciation. Columbia University Press, NY

    Book  Google Scholar 

  9. Leitch IJ, Bennett MD (1997) Polyploidy in angiosperms. Trends Plant Sci 2:470–476

    Article  Google Scholar 

  10. Guerra M (2008) Chromosome numbers in plant cytotaxonomy: concepts and implications. Cytogenet Genome Res 120:339–350

    Article  CAS  PubMed  Google Scholar 

  11. Dodsworth S, Chase MW, Leitch AR (2016) Is post-polyploidization diploidization the key to the evolutionary success of angiosperms? Bot J Linn Soc 180:1–5

    Article  Google Scholar 

  12. Carta A, Bedini G, Peruzzi L (2020) A deep dive into the ancestral chromosome number and genome size of flowering plants. New Phytol 228:1097–1106

    Article  CAS  PubMed  Google Scholar 

  13. Escudero M, Wendel JF (2020) The grand sweep of chromosomal evolution in angiosperms. New Phytol 228:805–808

    Article  PubMed  Google Scholar 

  14. Vargas P, McAllister HA, Morton C, Jury SL, Wilkinson MJ (1999) Polyploid speciation in Hedera (Araliaceae): phylogenetic and biogeographic insights based on chromosome counts and ITS sequences. Plant Syst Evol 219:165–179

    Google Scholar 

  15. Wang W, Lan H (2000) Rapid and parallel chromosomal number reductions in muntjac deer inferred from mitochondrial DNA phylogeny. Mol Biol Evol 17:1326–1333

    Article  CAS  PubMed  Google Scholar 

  16. Ohi-Toma T, Sugawara T, Murata H, Wanke S, Neinhuis C, Murata J (2006) Molecular phylogeny of Aristolochia sensu lato (Aristolochiaceae) based on sequences of rbcL, matK, and phyA genes, with special reference to differentiation of chromosome numbers. Syst Bot 31:481–492

    Google Scholar 

  17. Bena G, Prosperi JM, Lejeune B, Olivieri I (1998) Evolution of annual species of the genus Medicago: a molecular phylogenetic approach. Mol Phylogenet Evol 9:552–559

    Google Scholar 

  18. Cerbah M, Souza-Chies T, Jubier MF, Lejeune B, Siljak-Yakovlev S (1998) Molecular phylogeny of the genus Hypochaeris using internal transcribed spacers of nuclear rDNA: inference for chromosomal evolution. Mol Biol Evol 15:345–354

    Google Scholar 

  19. Watanabe K, Yahara T, Denda T, Kosuge K (1999) Chromosomal evolution in the genus Brachyscome (Asteraceae, Astereae): statistical tests regarding correlation between changes in karyotype and habit using phylogenetic information. J Plant Res 112:145–161

    Google Scholar 

  20. Aoki S, Ito M (2000) Molecular phylogeny of Nicotiana (Solanaceae) based on the nucleotide sequence of the matK gene. Plant Biol 2:316–324

    Google Scholar 

  21. Bakker FT, Culham A, Pankhurst CE, Gibby M (2000) Mitochondrial and chloroplast DNA-based phylogeny of Pelargonium (Geraniaceae). Am J Bot 87:727–734

    Google Scholar 

  22. Martel E, Poncet V, Lamy F, Siljak-Yakovlev S, Lejeune B, Sarr A (2004) Chromosome evolution of Pennisetum species (Poaceae): implications of ITS phylogeny. Plant Syst Evol 249:139–149

    Google Scholar 

  23. Hansen AK, Gilbert LE, Simpson BB, Downie SR, Cervi AC, Jansen RK (2006) Phylogenetic relationships and chromosome number evolution in Passiflora. Syst Bot 31:138–150

    Google Scholar 

  24. Mayrose I, Barker MS, Otto SP (2010) Probabilistic models of chromosome number evolution and the inference of polyploidy. Syst Biol 59:132–144

    Article  PubMed  Google Scholar 

  25. Koshi JM, Goldstein RA (1996) Probabilistic reconstruction of ancestral protein sequences. J Mol Evol 42:313–320

    Article  CAS  PubMed  Google Scholar 

  26. Pupko T, Pe I, Shamir R, Graur D (2000) A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol 17:890–896

    Article  CAS  PubMed  Google Scholar 

  27. Höhna S, Landis MJ, Heath TA, Boussau B, Lartillot N, Moore BR et al (2016) RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Syst Biol 65:726–736

    Article  PubMed  PubMed Central  Google Scholar 

  28. Mayrose I, Zhan SH, Rothfels CJ, Magnuson-Ford K, Barker MS, Rieseberg LH, Otto SP (2011) Recently formed polyploid plants diversify at lower rates. Sciences 333:1257–1257

    Article  CAS  Google Scholar 

  29. Soltis DE, Segovia-Salcedo MC, Jordon-Thaden I, Majure L, Miles NM, Mavrodiev EV et al (2014) Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayrose et al. (2011). New Phytol 202:1105–1117

    Article  PubMed  Google Scholar 

  30. Mayrose I, Zhan SH, Rothfels CJ, Arrigo N, Barker MS, Rieseberg LH, Otto SP (2015) Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis et al. (2014). New Phytol 206:27–35

    Article  PubMed  Google Scholar 

  31. Albertin W, Marullo P (2012) Polyploidy in fungi: evolution after whole-genome duplication. Proc R Soc B: Biol Sci 279:2497–2509

    Article  Google Scholar 

  32. Zhan SH, Glick L, Tsigenopoulos CS, Otto SP, Mayrose I (2014) Comparative analysis reveals that polyploidy does not decelerate diversification in fish. J Evol Biol 27:391–403

    Article  CAS  PubMed  Google Scholar 

  33. Glick L, Mayrose I (2014) ChromEvol: assessing the pattern of chromosome number evolution and the inference of polyploidy along a phylogeny. Mol Biol Evol 31:1914–1922

    Article  CAS  PubMed  Google Scholar 

  34. Zenil-Ferguson R, Ponciano JM, Burleigh JG (2017) Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots. Evolution 71:1138–1148

    Article  CAS  PubMed  Google Scholar 

  35. Zenil-Ferguson R, Burleigh JG, Ponciano JM (2018) Chromploid: an R package for chromosome number evolution across the plant tree of life. Appl Plant Sci 6:e1037

    Article  PubMed  PubMed Central  Google Scholar 

  36. Blackmon H, Justison J, Mayrose I, Goldberg EE (2019) Meiotic drive shapes rates of karyotype evolution in mammals. Evolution 73:511–523

    Article  PubMed  PubMed Central  Google Scholar 

  37. Maddison WP, Midford PE, Otto SP (2007) Estimating a binary character’s effect on speciation and extinction. Syst Biol 56:701–710

    Article  PubMed  Google Scholar 

  38. Márquez-Corro JI, Martín-Bravo S, Spalink D, Luceño M, Escudero M (2019) Inferring hypothesis-based transitions in clade-specific models of chromosome number evolution in sedges (Cyperaceae). Mol Phylogenet Evol 135:203–209

    Article  PubMed  Google Scholar 

  39. O'Meara BC, Ané C, Sanderson MJ, Wainwright PC (2006) Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922–933

    PubMed  Google Scholar 

  40. Escudero M, Hipp AL (2013) Shifts in diversification rates and clade ages explain species richness in higher-level sedge taxa (Cyperaceae). Am J Bot 100:2403–2411

    Article  PubMed  Google Scholar 

  41. Spalink D, Drew BT, Pace MC, Zaborsky JG, Starr JR, Cameron KM et al (2016) Biogeography of the cosmopolitan sedges (Cyperaceae) and the area-richness correlation in plants. J Biogeogr 43:1893–1904

    Article  Google Scholar 

  42. Aparicio A, Escudero M, Valdés-Florido A, Pachón M, Rubio E, Albaladejo RG et al (2019) Karyotype evolution in Helianthemum (Cistaceae): dysploidy, achiasmate meiosis and ecological specialization in H. squamatum, a true gypsophile. Bot J Linn Soc 191:484–501

    Article  Google Scholar 

  43. Eastman JM, Alfaro ME, Joyce P, Hipp AL, Harmon LJ (2011) A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution 65:3578–3589

    Article  PubMed  Google Scholar 

  44. Stack JC, Harmon LJ, O'Meara B (2011) RBrownie: an R package for testing hypotheses about rates of evolutionary change. Methods Ecol Evol 2:660–662

    Article  Google Scholar 

  45. Rabosky DL, Santini F, Eastman J, Smith SA, Sidlauskas B, Chang J, Alfaro ME (2013) Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat Commun 4:1–8

    Article  Google Scholar 

  46. Uyeda JC, Harmon LJ (2014) A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data. Syst Biol 63:902–918

    Article  PubMed  Google Scholar 

  47. Ingram T, Mahler DL (2013) SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion. Methods Ecol Evol 4:416–425

    Article  Google Scholar 

  48. Freyman WA, Höhna S (2018) Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach. Syst Biol 67:195–215

    Article  PubMed  Google Scholar 

  49. Mansion G, Struwe L (2004) Generic delimitation and phylogenetic relationships within the subtribe Chironiinae (Chironieae: Gentianaceae), with special reference to Centaurium: evidence from nrDNA and cpDNA sequences. Mol Phylogenet Evol 32:951–977

    Google Scholar 

  50. Díaz-Lifante Z (2012) Centaurium in Flora Iberica 11, 49–81. Romero C, Quintanar A (eds). Real Jardín Botánico-CSIC Press, Madrid

    Google Scholar 

  51. Zeltner L (1970) Recherches de biosystématique Sur les genres Blackstonia Huds. et Centaurium Hill (Gentianaceae). Bull Soc Neuchâteloise Sci Nat 93:1–164

    Google Scholar 

  52. Mansion G, Zeltner L, Bretagnolle F (2005) Phylogenetic patterns and polyploid evolution within the Mediterranean genus Centaurium (Gentianaceae - Chironieae). Taxon 54:931–950

    Article  Google Scholar 

  53. Maguilla E, Escudero M, Jiménez-Lobato V, Díaz-Lifante Z, Andrés-Camacho C, Arroyo J (2021) Polyploidy expands the range of Centaurium (Gentianaceae). Front Plant Sci 12:650551

    Google Scholar 

  54. Pagel M (1994) Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc R Soc London Ser B: Biol Sci 255:37–45

    Article  Google Scholar 

  55. Rabosky DL, Goldberg EE (2015) Model inadequacy and mistaken inferences of trait-dependent speciation. Syst Biol 64:340–355

    Article  CAS  PubMed  Google Scholar 

  56. Beaulieu JM, O'Meara BC, Donoghue MJ (2013) Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms. Syst Biol 62:725–737

    Article  PubMed  Google Scholar 

  57. Beaulieu JM, O’Meara BC (2016) Detecting hidden diversification shifts in models of trait-dependent speciation and extinction. Syst Biol 65:583–601

    Article  PubMed  Google Scholar 

  58. Landis JB, Soltis DE, Li Z, Marx HE, Barker MS, Tank DC, Soltis PS (2018) Impact of whole-genome duplication events on diversification rates in angiosperms. Am J Bot 105:348–363

    Article  PubMed  Google Scholar 

  59. Wendel JF (2015) The wondrous cycles of polyploidy in plants. Am J Bot 102:1753–1756

    Article  CAS  PubMed  Google Scholar 

  60. Hallinan NM, Lindberg DR (2011) Comparative analysis of chromosome counts infers three paleopolyploidies in the mollusca. Genome Biol Evol 3:1150–1163

    Article  PubMed  PubMed Central  Google Scholar 

  61. Zenil-Ferguson R, Ponciano JM, Burleigh JG (2016) Evaluating the role of genome downsizing and size thresholds from genome size distributions in angiosperms. Am J Bot 103:1175–1186

    Article  PubMed  Google Scholar 

  62. Matzke NJ (2013) Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing. Front Biogeogr 5:242–248

    Google Scholar 

  63. Tribble CM, Freyman WA, Lim JY, Landis MJ, Barido-Sottani J, Kopperud BT et al (2021) RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes. bioRxiv

    Google Scholar 

Download references

Acknowledgments

This work was supported by a grant to ME (MICINN, PGC2018-099608-B-I00). We thank the Andalusian Scientific Information Technology Center (CICA, Seville, Spain) for providing computational and research resources.

Author information

Authors and Affiliations

  1. Department of Plant Biology and Ecology, University of Seville, Seville, Spain

    Marcial Escudero

  2. Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain

    Enrique Maguilla, José Ignacio Márquez-Corro & Santiago Martín-Bravo

  3. School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel

    Itay Mayrose & Anat Shafir

  4. Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, China

    Lu Tan

  5. Department of Biology, University of Kentucky, Lexington, KY, USA

    Rosana Zenil-Ferguson

  6. School of Life Sciences, University of Hawai`i at Mānoa, Honolulu, HI, USA

    Carrie Tribble

Authors
  1. Marcial Escudero
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Enrique Maguilla
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. José Ignacio Márquez-Corro
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Santiago Martín-Bravo
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Itay Mayrose
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Anat Shafir
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Lu Tan
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Carrie Tribble
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Rosana Zenil-Ferguson
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Institute of Botany, TU Dresden, Dresden, Germany

    Tony Heitkam

  2. Botanical Institute of Barcelona, Barcelona, Spain

    Sònia Garcia

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Escudero, M. et al. (2023). Using ChromEvol to Determine the Mode of Chromosomal Evolution. In: Heitkam, T., Garcia, S. (eds) Plant Cytogenetics and Cytogenomics. Methods in Molecular Biology, vol 2672. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3226-0_32

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-3226-0_32

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3225-3

  • Online ISBN: 978-1-0716-3226-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation